FetalBrain - Gestational week associated analysis

Updated: Tue Jan 6 15:53:19 2015

DMR identification with methyl_diff

• Identify DM CpGs
  • methyl_diff one-sided p-value \(\le\) 0.005
    
  • delta fractional methylation \(\ge\) 0.5
    
  • fractional methylation of one sample \(\ge\) 0.75
    
• Collapse DM CpGs into DMRs
  • adjacent DM CpGs have the same DM status;
    
  • distance between adjacent CpGs (size) \(\le\) 300bp;
    
  • No. of CpGs within each DMR \(\ge\) 3.

Background

UMR summary and sanity check

• On average, there are 1692 17-week UMRs, 428 intersect between Cortex and GE, and 450 13-week UMRs, 76 intersect. The intersect is highly significant.
  
• Median DMR length is 321, comparable to breast. It’s similar in all chromosomes in 17-week UMRs, but fluctuate more in 13-week UMRs, probably due to small No. of UMRs identified.
  
• Median No. of CpGs per DMR is 5, also similar to breast.

Sample	Total.DMR	Hyper.DMR	Hypo.DMR
Cortex-HuFNSC02_Cortex-HuFNSC04	1283	179	1104
GE-HuFNSC02_GE-HuFNSC04	3002	722	2280

UMR asymmetry

• On average, there are , 4.8-fold enrichment in total UMR frequency in 17-week compared to 13-week, 8.17 in Cortex, and 3.97 in GE.

GREAT enrichment for GW-associated UMRs

• GREAT terms are strongly associated with neuron differentiation and brain development.
  
• 17-week UMRs are highly enriched in glial cell development in Cortex, and neural tube development in GE. Intersect of these two cell types show enrichment in cell fate commitment related to different types of brain cells.
  
• 13-week UMRs are enriched in neuron fate commitment in Cortex, and regionalization in GE. Intersect of these two cell types show no significant enrichment.

UMR Genomic breakdown

• On average, 62.26% of CpGs in UMRs overlap with genebody, and 23.95% of CpGs in UMRs overlap with promoters, 1.78-fold enriched. 44.87% of CpGs in UMRs overlap with CGIs, 5.97-fold than expected by random.

Proximal UMRs and DE genes

• On average, there are 165 UMRs proximally (TSS +/- 1.5kb) associated with protein-coding genes, 18.23% in 17-week UMRs, and 4.88% in 13-week UMRs, much lower than 17-week UMRs.
  
• Among proximal UMRs, 14.26% of 17-week proximal UMRs are associated with DE genes, 13.64% 13-week UMRs, similar to 17-week UMRs. On average, 20 DE genes are associated with GW UMRs.
  
• Among proximal UMR assocaited with DE genes, 79.55% 17-week UMRs change in the same direction as DE genes (hyper to DN), much higher than any Fetal Brain UMRs and close to observed in breast. 50% in 13-week UMRs, much lower than 17-week UMRs.

	proximal.DMRs	unique.genes	DE.DMRs	unique.DE.genes	same.direction
Cortex04.UMRs	7	7	0	0	0
Cortex02.UMRs	215	215	24	19	21
GE04.UMRs	37	36	6	5	3
GE02.UMRs	402	402	64	57	49

Proximal 13-week UMRs in both Cortex and GE

id	name	description
ENSG00000189334	S100A14	S100_calcium_binding_protein_A14_[Source:HGNC_Symbol;Acc:18901]
ENSG00000237693	IRGM	immunity-related_GTPase_family,M[Source:HGNC_Symbol;Acc:29597]
ENSG00000124564	SLC17A3	solute_carrier_family_17_(sodium_phosphate),member3_[Source:HGNC_Symbol;Acc:10931]

Proximal GE 13-week UMRs with DE genes

id	name	description	DM	DE
ENSG00000134954	ETS1	v-ets_erythroblastosis_virus_E26_oncogene_homolog_1_(avian)_[Source:HGNC_Symbol;Acc:3488]	hyper	UP
ENSG00000136352	NKX2-1	NK2_homeobox_1_[Source:HGNC_Symbol;Acc:11825]	hyper	UP
ENSG00000165588	OTX2	orthodenticle_homeobox_2_[Source:HGNC_Symbol;Acc:8522]	hyper	UP
ENSG00000231421			hyper	DN
ENSG00000155760	FZD7	frizzled_family_receptor_7_[Source:HGNC_Symbol;Acc:4045]	hyper	DN

Proximal 17-week UMRs with DE genes in both Cortex and GE

id	name	description	DM	DE
ENSG00000255737	NA	HCG2014417,isoformCRA_aUncharacterized_proteincDNA_FLJ59598_[Source:UniProtKB/TrEMBL;Acc:B7Z718]	hypo	UP
ENSG00000167178	ISLR2	immunoglobulin_superfamily_containing_leucine-rich_repeat_2_[Source:HGNC_Symbol;Acc:29286]	hypo	UP
ENSG00000161999	JMJD8	jumonji_domain_containing_8_[Source:HGNC_Symbol;Acc:14148]	hypo	UP
ENSG00000051523	CYBA	cytochrome_b-245,alphapolypeptide_[Source:HGNC_Symbol;Acc:2577]	hypo	UP
ENSG00000169515	CCDC8	coiled-coil_domain_containing_8_[Source:HGNC_Symbol;Acc:25367]	hypo	UP
ENSG00000205927	OLIG2	oligodendrocyte_lineage_transcription_factor_2_[Source:HGNC_Symbol;Acc:9398]	hypo	UP
ENSG00000189060	H1F0	H1_histone_family,member0_[Source:HGNC_Symbol;Acc:4714]	hypo	UP
ENSG00000146904	EPHA1	EPH_receptor_A1_[Source:HGNC_Symbol;Acc:3385]	hypo	UP
ENSG00000165072	MAMDC2	MAM_domain_containing_2_[Source:HGNC_Symbol;Acc:23673]	hypo	UP

UMRs overlapping with TFBS

TF	UMR17week_Cortex	UMR13week_Cortex	Ratio_Cortex	UMR17week_GE	UMR13week_GE	Ratio_GE
MAZ	133	5	26.6000	319	12	26.5833
GTF2F1	28	1	28.0000	103	2	51.5000
ZBTB7A	97	3	32.3333	201	3	67.0000
HMGN3	66	2	33.0000	131	4	32.7500
NRF1	34	1	34.0000	64	1	64.0000
MXI1	112	3	37.3333	262	7	37.4286
E2F4	50	1	50.0000	110	1	110.0000
CCNT2	87	1	87.0000	148	4	37.0000
E2F6	140	1	140.0000	263	8	32.8750

UMR enrichment at chromosome ends

DE genes summary

• On average, there are 561 genes differentially expressed between 13- and 17-week individuals, NA DE between GW13 and GW15 individuals, NA DE between GW15 and GW17, NA DE between GW13 and GW17.
  
• Within each cell type, majority of DE genes are shared among different comparisons (hypergeometric p-value = 0), less but still significant genes overlap between cell types. .
  
• Majority of the GW-associated DE genes are stage-specific.

	UP	DN	DE	GW	type	Sample
1	284	281	565	GW17-GW15	cortex	GW17-GW15.1_cortex
2	365	165	530	GW17-GW13	cortex	GW17-GW13.1_cortex
3	398	283	681	GW17-GW15	cortex	GW17-GW15.2_cortex
4	497	225	722	GW17-GW13	cortex	GW17-GW13.2_cortex
5	459	183	642	GW15-GW13	cortex	GW15-GW13_cortex
6	587	274	861	GW17-GW15	GE	GW17-GW15.1_GE
7	645	238	883	GW17-GW13	GE	GW17-GW13.1_GE
8	609	312	921	GW17-GW15	GE	GW17-GW15.2_GE
9	610	259	869	GW17-GW13	GE	GW17-GW13.2_GE
10	313	232	545	GW15-GW13	GE	GW15-GW13_GE
11	74	75	173	GW17-GW15	shared	GW17-GW15.1_shared
12	239	65	311	GW17-GW13	shared	GW17-GW13.1_shared
13	78	75	180	GW17-GW15	shared	GW17-GW15.2_shared
14	282	84	372	GW17-GW13	shared	GW17-GW13.2_shared
15	79	74	166	GW15-GW13	shared	GW15-GW13_shared

Stage-specific DE gene profiles

• Cortex stage-specific DE genes are mostly turned on during GW13-GW15, while GE stage-specific DE genes are mostly turned on during GW15-GW17. This supports the clustering in coding gene RPKM, exon RPKM and miRNA RPM that in cortex GW15 clustered with GW17, and in GE GW15 clustered with GW13.

• Genes activated during GW13-GW15 in cortex, not GE
  

  id	name	description
  ENSG00000086570	FAT2	FAT_tumor_suppressor_homolog_2_(Drosophila)_[Source:HGNC_Symbol;Acc:3596]
  ENSG00000117152	RGS4	regulator_of_G-protein_signaling_4_[Source:HGNC_Symbol;Acc:10000]
  ENSG00000204577	LILRB3	leukocyte_immunoglobulin-like_receptor,subfamilyB_(with_TM_and_ITIM_domains),member3_[Source:HGNC_Symbol;Acc:6607]
  ENSG00000115353	TACR1	tachykinin_receptor_1_[Source:HGNC_Symbol;Acc:11526]
  ENSG00000117281	CD160	CD160_molecule_[Source:HGNC_Symbol;Acc:17013]
  ENSG00000144130	NT5DC4	5’-nucleotidase_domain_containing_4_[Source:HGNC_Symbol;Acc:27678]
  ENSG00000166501	PRKCB	protein_kinase_C,beta[Source:HGNC_Symbol;Acc:9395]
  ENSG00000074276	CDHR2	cadherin-related_family_member_2_[Source:HGNC_Symbol;Acc:18231]
  ENSG00000185105	MYADML2	myeloid-associated_differentiation_marker-like_2_[Source:HGNC_Symbol;Acc:34548]
  ENSG00000075073	TACR2	tachykinin_receptor_2_[Source:HGNC_Symbol;Acc:11527]
  ENSG00000206129	NA	HCG2045177Uncharacterized_proteincDNA_FLJ45743_fis,cloneKIDNE2016464_[Source:UniProtKB/TrEMBL;Acc:Q6ZS83]
  ENSG00000138653	NDST4	N-deacetylase/N-sulfotransferase_(heparan_glucosaminyl)4[Source:HGNC_Symbol;Acc:20779]
  ENSG00000163357	DCST1	DC-STAMP_domain_containing_1_[Source:HGNC_Symbol;Acc:26539]
  ENSG00000171873	ADRA1D	adrenergic,alpha-1D-,receptor_[Source:HGNC_Symbol;Acc:280]
  ENSG00000212122	TSSK1B	testis-specific_serine_kinase_1B_[Source:HGNC_Symbol;Acc:14968]
  ENSG00000186583	SPATC1	spermatogenesis_and_centriole_associated_1_[Source:HGNC_Symbol;Acc:30510]
  ENSG00000204323	C17orf109	chromosome_17_open_reading_frame_109_[Source:HGNC_Symbol;Acc:40030]
  ENSG00000116176	TPSG1	tryptase_gamma_1_[Source:HGNC_Symbol;Acc:14134]
  ENSG00000128617	OPN1SW	opsin_1_(cone_pigments),short-wave-sensitive[Source:HGNC_Symbol;Acc:1012]
  ENSG00000156113	KCNMA1	potassium_large_conductance_calcium-activated_channel,subfamilyM,alphamember_1_[Source:HGNC_Symbol;Acc:6284]
  ENSG00000006453	NA	Brain-specific_angiogenesis_inhibitor_1-associated_protein_2-like_protein_1_[Source:UniProtKB/Swiss-Prot;Acc:Q9UHR4]
  ENSG00000166278	C2	complement_component_2_[Source:HGNC_Symbol;Acc:1248]
  ENSG00000233198	RNF224	ring_finger_protein_224_[Source:HGNC_Symbol;Acc:41912]
  ENSG00000146221	TCTE1	t-complex-associated-testis-expressed_1_[Source:HGNC_Symbol;Acc:11693]
  ENSG00000149609	C20orf144	chromosome_20_open_reading_frame_144_[Source:HGNC_Symbol;Acc:16137]
  ENSG00000233745
  ENSG00000135436	FAM186B	family_with_sequence_similarity_186,memberB_[Source:HGNC_Symbol;Acc:25296]
  ENSG00000218416	NA	Uncharacterized_protein_[Source:UniProtKB/TrEMBL;Acc:B5MC12]
  ENSG00000130173	C19orf80	chromosome_19_open_reading_frame_80_[Source:HGNC_Symbol;Acc:24933]
  ENSG00000176563	CNTD1	cyclin_N-terminal_domain_containing_1_[Source:HGNC_Symbol;Acc:26847]
  ENSG00000130812	ANGPTL6	angiopoietin-like_6_[Source:HGNC_Symbol;Acc:23140]
  ENSG00000161509	GRIN2C	glutamate_receptor,ionotropic,N-methyl_D-aspartate_2C_[Source:HGNC_Symbol;Acc:4587]
  ENSG00000095303	PTGS1	prostaglandin-endoperoxide_synthase_1_(prostaglandin_G/H_synthase_and_cyclooxygenase)_[Source:HGNC_Symbol;Acc:9604]
  ENSG00000125845	BMP2	bone_morphogenetic_protein_2_[Source:HGNC_Symbol;Acc:1069]
  ENSG00000137752	CASP1	caspase_1,apoptosis-relatedcysteine_peptidase_(interleukin_1,beta,convertase)_[Source:HGNC_Symbol;Acc:1499]
  ENSG00000141682	PMAIP1	phorbol-12-myristate-13-acetate-induced_protein_1_[Source:HGNC_Symbol;Acc:9108]
  ENSG00000163394	CCKAR	cholecystokinin_A_receptor_[Source:HGNC_Symbol;Acc:1570]
  ENSG00000124529	HIST1H4B	histone_cluster_1,H4b[Source:HGNC_Symbol;Acc:4789]
  ENSG00000140015	KCNH5	potassium_voltage-gated_channel,subfamilyH_(eag-related),member5_[Source:HGNC_Symbol;Acc:6254]
  ENSG00000182572	HIST1H3I	histone_cluster_1,H3i[Source:HGNC_Symbol;Acc:4771]
  ENSG00000083067	TRPM3	transient_receptor_potential_cation_channel,subfamilyM,member3_[Source:HGNC_Symbol;Acc:17992]
  ENSG00000172497	ACOT12	acyl-CoA_thioesterase_12_[Source:HGNC_Symbol;Acc:24436]
  ENSG00000166922	SCG5	secretogranin_V_(7B2_protein)_[Source:HGNC_Symbol;Acc:10816]
  ENSG00000183569	SERHL2	serine_hydrolase-like_2_[Source:HGNC_Symbol;Acc:29446]
  ENSG00000136960	ENPP2	ectonucleotide_pyrophosphatase/phosphodiesterase_2_[Source:HGNC_Symbol;Acc:3357]
  ENSG00000005884	ITGA3	integrin,alpha3_(antigen_CD49C,alpha3_subunit_of_VLA-3_receptor)_[Source:HGNC_Symbol;Acc:6139]
  ENSG00000197182	MIR4763	microRNA_4763_[Source:HGNC_Symbol;Acc:41677]
  ENSG00000169715	MT1E	metallothionein_1E_[Source:HGNC_Symbol;Acc:7397]
  ENSG00000175592	FOSL1	FOS-like_antigen_1_[Source:HGNC_Symbol;Acc:13718]
  ENSG00000115107	STEAP3	STEAP_family_member_3,metalloreductase[Source:HGNC_Symbol;Acc:24592]
  ENSG00000117877	CD3EAP	CD3e_molecule,epsilonassociated_protein_[Source:HGNC_Symbol;Acc:24219]
  ENSG00000156049	GNA14	guanine_nucleotide_binding_protein_(G_protein),alpha14_[Source:HGNC_Symbol;Acc:4382]
  ENSG00000241978	AKAP2	A_kinase_(PRKA)anchorprotein_2_[Source:HGNC_Symbol;Acc:372]
  ENSG00000157654	PALM2-AKAP2	PALM2-AKAP2_readthrough_[Source:HGNC_Symbol;Acc:33529]
  ENSG00000169231	THBS3	thrombospondin_3_[Source:HGNC_Symbol;Acc:11787]
  ENSG00000112309	B3GAT2	beta-1,3-glucuronyltransferase_2_(glucuronosyltransferase_S)_[Source:HGNC_Symbol;Acc:922]
  ENSG00000158457	TSPAN33	tetraspanin_33_[Source:HGNC_Symbol;Acc:28743]
  ENSG00000135926	TMBIM1	transmembrane_BAX_inhibitor_motif_containing_1_[Source:HGNC_Symbol;Acc:23410]
  ENSG00000075340	ADD2	adducin_2_(beta)_[Source:HGNC_Symbol;Acc:244]
  ENSG00000134138	MEIS2	Meis_homeobox_2_[Source:HGNC_Symbol;Acc:7001]
  ENSG00000152642	GPD1L	glycerol-3-phosphate_dehydrogenase_1-like_[Source:HGNC_Symbol;Acc:28956]
  ENSG00000131941	RHPN2	rhophilin,RhoGTPase_binding_protein_2_[Source:HGNC_Symbol;Acc:19974]
  ENSG00000111859	NEDD9	neural_precursor_cell_expressed,developmentallydown-regulated_9_[Source:HGNC_Symbol;Acc:7733]
  ENSG00000171189	GRIK1	glutamate_receptor,ionotropic,kainate_1_[Source:HGNC_Symbol;Acc:4579]
  ENSG00000149218	ENDOD1	endonuclease_domain_containing_1_[Source:HGNC_Symbol;Acc:29129]
  ENSG00000100410	PHF5A	PHD_finger_protein_5A_[Source:HGNC_Symbol;Acc:18000]
  ENSG00000228716	DHFR	dihydrofolate_reductase_[Source:HGNC_Symbol;Acc:2861]
  ENSG00000158623	COPG2	coatomer_protein_complex,subunitgamma_2_[Source:HGNC_Symbol;Acc:2237]
  ENSG00000162490	C1orf187	chromosome_1_open_reading_frame_187_[Source:HGNC_Symbol;Acc:25054]
  ENSG00000181350	C17orf76	chromosome_17_open_reading_frame_76_[Source:HGNC_Symbol;Acc:32403]
  ENSG00000185386	MAPK11	mitogen-activated_protein_kinase_11_[Source:HGNC_Symbol;Acc:6873]
  ENSG00000155893	ACPL2	acid_phosphatase-like_2_[Source:HGNC_Symbol;Acc:26303]
  ENSG00000150938	CRIM1	cysteine_rich_transmembrane_BMP_regulator_1_(chordin-like)_[Source:HGNC_Symbol;Acc:2359]
  ENSG00000166337	TAF10	TAF10_RNA_polymerase_II,TATAbox_binding_protein_(TBP)-associated_factor,30kDa[Source:HGNC_Symbol;Acc:11543]
  ENSG00000198873	GRK5	G_protein-coupled_receptor_kinase_5_[Source:HGNC_Symbol;Acc:4544]
  ENSG00000102271	KLHL4	kelch-like_4_(Drosophila)_[Source:HGNC_Symbol;Acc:6355]
  ENSG00000172380	GNG12	guanine_nucleotide_binding_protein_(G_protein),gamma12_[Source:HGNC_Symbol;Acc:19663]
  ENSG00000110107	PRPF19	PRP19/PSO4_pre-mRNA_processing_factor_19_homolog_(S.cerevisiae)[Source:HGNC_Symbol;Acc:17896]
  ENSG00000162975	KCNF1	potassium_voltage-gated_channel,subfamilyF,member1_[Source:HGNC_Symbol;Acc:6246]
  ENSG00000114942	EEF1B2	eukaryotic_translation_elongation_factor_1_beta_2_[Source:HGNC_Symbol;Acc:3208]
  ENSG00000139970	RTN1	reticulon_1_[Source:HGNC_Symbol;Acc:10467]
  ENSG00000205609	EIF3CL	eukaryotic_translation_initiation_factor_3,subunitC-like_[Source:HGNC_Symbol;Acc:26347]
  ENSG00000164929	BAALC	brain_and_acute_leukemia,cytoplasmic[Source:HGNC_Symbol;Acc:14333]

• Genes activated during GW15-GW17 in GE, not cortex
  

  id	name	description
  ENSG00000154736	ADAMTS5	ADAM_metallopeptidase_with_thrombospondin_type_1_motif,5[Source:HGNC_Symbol;Acc:221]
  ENSG00000159263	SIM2	single-minded_homolog_2_(Drosophila)_[Source:HGNC_Symbol;Acc:10883]
  ENSG00000163285	GABRG1	gamma-aminobutyric_acid_(GABA)Areceptor,gamma1_[Source:HGNC_Symbol;Acc:4086]
  ENSG00000169994	MYO7B	myosin_VIIB_[Source:HGNC_Symbol;Acc:7607]
  ENSG00000182836	PLCXD3	phosphatidylinositol-specific_phospholipase_C,Xdomain_containing_3_[Source:HGNC_Symbol;Acc:31822]
  ENSG00000118733	OLFM3	olfactomedin_3_[Source:HGNC_Symbol;Acc:17990]
  ENSG00000176769	TCERG1L	transcription_elongation_regulator_1-like_[Source:HGNC_Symbol;Acc:23533]
  ENSG00000107099	DOCK8	dedicator_of_cytokinesis_8_[Source:HGNC_Symbol;Acc:19191]
  ENSG00000179542	SLITRK4	SLIT_and_NTRK-like_family,member4_[Source:HGNC_Symbol;Acc:23502]
  ENSG00000187775	DNAH17	dynein,axonemal,heavy_chain_17_[Source:HGNC_Symbol;Acc:2946]
  ENSG00000250493	NA	Uncharacterized_protein_[Source:UniProtKB/TrEMBL;Acc:E9PLU8]
  ENSG00000101188	NTSR1	neurotensin_receptor_1_(high_affinity)_[Source:HGNC_Symbol;Acc:8039]
  ENSG00000119608	PROX2	prospero_homeobox_2_[Source:HGNC_Symbol;Acc:26715]
  ENSG00000215475	SIAH3	seven_in_absentia_homolog_3_(Drosophila)_[Source:HGNC_Symbol;Acc:30553]
  ENSG00000164588	HCN1	hyperpolarization_activated_cyclic_nucleotide-gated_potassium_channel_1_[Source:HGNC_Symbol;Acc:4845]
  ENSG00000196104	SPOCK3	sparc/osteonectin,cwcvand_kazal-like_domains_proteoglycan_(testican)3[Source:HGNC_Symbol;Acc:13565]
  ENSG00000132677	RHBG	Rh_family,Bglycoprotein_(gene/pseudogene)_[Source:HGNC_Symbol;Acc:14572]
  ENSG00000137573	SULF1	sulfatase_1_[Source:HGNC_Symbol;Acc:20391]
  ENSG00000185245	GP1BA	glycoprotein_Ib_(platelet),alphapolypeptide_[Source:HGNC_Symbol;Acc:4439]
  ENSG00000117154	IGSF21	immunoglobin_superfamily,member21_[Source:HGNC_Symbol;Acc:28246]
  ENSG00000172215	CXCR6	chemokine_(C-X-C_motif)receptor6_[Source:HGNC_Symbol;Acc:16647]
  ENSG00000172404	DNAJB7	DnaJ_(Hsp40)homolog,subfamily_B,member7_[Source:HGNC_Symbol;Acc:24986]
  ENSG00000172568	FNDC9	fibronectin_type_III_domain_containing_9_[Source:HGNC_Symbol;Acc:33547]
  ENSG00000019505	SYT13	synaptotagmin_XIII_[Source:HGNC_Symbol;Acc:14962]
  ENSG00000166006	KCNC2	potassium_voltage-gated_channel,Shaw-relatedsubfamily,member2_[Source:HGNC_Symbol;Acc:6234]
  ENSG00000170162	VGLL2	vestigial_like_2_(Drosophila)_[Source:HGNC_Symbol;Acc:20232]
  ENSG00000174171	NA	HCG1998685_[Source:UniProtKB/TrEMBL;Acc:Q8TCB4]
  ENSG00000235531	NA	Uncharacterized_proteincDNA_FLJ53548_[Source:UniProtKB/TrEMBL;Acc:B7Z945]
  ENSG00000140945	CDH13	cadherin_13,H-cadherin(heart)_[Source:HGNC_Symbol;Acc:1753]
  ENSG00000169314	C22orf15	chromosome_22_open_reading_frame_15_[Source:HGNC_Symbol;Acc:15558]
  ENSG00000182463	TSHZ2	teashirt_zinc_finger_homeobox_2_[Source:HGNC_Symbol;Acc:13010]
  ENSG00000203691
  ENSG00000171819	ANGPTL7	angiopoietin-like_7_[Source:HGNC_Symbol;Acc:24078]
  ENSG00000011677	GABRA3	gamma-aminobutyric_acid_(GABA)Areceptor,alpha3_[Source:HGNC_Symbol;Acc:4077]
  ENSG00000100146	SOX10	SRY_(sex_determining_region_Y)-box_10_[Source:HGNC_Symbol;Acc:11190]
  ENSG00000132031	MATN3	matrilin_3_[Source:HGNC_Symbol;Acc:6909]
  ENSG00000138722	MMRN1	multimerin_1_[Source:HGNC_Symbol;Acc:7178]
  ENSG00000156675	RAB11FIP1	RAB11_family_interacting_protein_1_(class_I)_[Source:HGNC_Symbol;Acc:30265]
  ENSG00000180071	ANKRD18A	ankyrin_repeat_domain_18A_[Source:HGNC_Symbol;Acc:23643]
  ENSG00000214872	SMTNL1	smoothelin-like_1_[Source:HGNC_Symbol;Acc:32394]
  ENSG00000019102	VSIG2	V-set_and_immunoglobulin_domain_containing_2_[Source:HGNC_Symbol;Acc:17149]
  ENSG00000255974	CYP2A6	cytochrome_P450,family2,subfamilyA,polypeptide6_[Source:HGNC_Symbol;Acc:2610]
  ENSG00000106341	PPP1R17	protein_phosphatase_1,regulatorysubunit_17_[Source:HGNC_Symbol;Acc:16973]
  ENSG00000106128	GHRHR	growth_hormone_releasing_hormone_receptor_[Source:HGNC_Symbol;Acc:4266]
  ENSG00000111249	CUX2	cut-like_homeobox_2_[Source:HGNC_Symbol;Acc:19347]
  ENSG00000133640	LRRIQ1	leucine-rich_repeats_and_IQ_motif_containing_1_[Source:HGNC_Symbol;Acc:25708]
  ENSG00000166359	WDR88	WD_repeat_domain_88_[Source:HGNC_Symbol;Acc:26999]
  ENSG00000180269	GPR139	G_protein-coupled_receptor_139_[Source:HGNC_Symbol;Acc:19995]
  ENSG00000182601	HS3ST4	heparan_sulfate_(glucosamine)3-O-sulfotransferase4_[Source:HGNC_Symbol;Acc:5200]
  ENSG00000205838	TTC23L	tetratricopeptide_repeat_domain_23-like_[Source:HGNC_Symbol;Acc:26355]
  ENSG00000110852	CLEC2B	C-type_lectin_domain_family_2,memberB_[Source:HGNC_Symbol;Acc:2053]
  ENSG00000134115	CNTN6	contactin_6_[Source:HGNC_Symbol;Acc:2176]
  ENSG00000134602	NA	Serine/threonine-protein_kinase_MST4_[Source:UniProtKB/Swiss-Prot;Acc:Q9P289]
  ENSG00000170571	EMB	embigin_[Source:HGNC_Symbol;Acc:30465]
  ENSG00000185862	EVI2B	ecotropic_viral_integration_site_2B_[Source:HGNC_Symbol;Acc:3500]
  ENSG00000179038
  ENSG00000164484	TMEM200A	transmembrane_protein_200A_[Source:HGNC_Symbol;Acc:21075]
  ENSG00000183032	SLC25A21	solute_carrier_family_25_(mitochondrial_oxodicarboxylate_carrier),member21_[Source:HGNC_Symbol;Acc:14411]
  ENSG00000091879	ANGPT2	angiopoietin_2_[Source:HGNC_Symbol;Acc:485]
  ENSG00000101292	PROKR2	prokineticin_receptor_2_[Source:HGNC_Symbol;Acc:15836]
  ENSG00000153071	DAB2	disabled_homolog_2,mitogen-responsivephosphoprotein_(Drosophila)_[Source:HGNC_Symbol;Acc:2662]
  ENSG00000184566	NA	HCG1785179PRO1787Uncharacterized_protein_[Source:UniProtKB/TrEMBL;Acc:Q9P1G6]
  ENSG00000154760	SLFN13	schlafen_family_member_13_[Source:HGNC_Symbol;Acc:26481]
  ENSG00000203811	HIST2H3C	histone_cluster_2,H3c[Source:HGNC_Symbol;Acc:20503]
  ENSG00000102053	ZC3H12B	zinc_finger_CCCH-type_containing_12B_[Source:HGNC_Symbol;Acc:17407]
  ENSG00000106236	NPTX2	neuronal_pentraxin_II_[Source:HGNC_Symbol;Acc:7953]
  ENSG00000186493	C5orf38	chromosome_5_open_reading_frame_38_[Source:HGNC_Symbol;Acc:24226]
  ENSG00000172123	SLFN12	schlafen_family_member_12_[Source:HGNC_Symbol;Acc:25500]
  ENSG00000178235	SLITRK1	SLIT_and_NTRK-like_family,member1_[Source:HGNC_Symbol;Acc:20297]
  ENSG00000197410	DCHS2	dachsous_2_(Drosophila)_[Source:HGNC_Symbol;Acc:23111]
  ENSG00000164100	NDST3	N-deacetylase/N-sulfotransferase_(heparan_glucosaminyl)3[Source:HGNC_Symbol;Acc:7682]
  ENSG00000033122	LRRC7	leucine_rich_repeat_containing_7_[Source:HGNC_Symbol;Acc:18531]
  ENSG00000073734	ABCB11	ATP-binding_cassette,sub-familyB_(MDR/TAP),member11_[Source:HGNC_Symbol;Acc:42]
  ENSG00000081479	LRP2	low_density_lipoprotein_receptor-related_protein_2_[Source:HGNC_Symbol;Acc:6694]
  ENSG00000203815	NA	UPF0627_protein_ENSP00000358171_[Source:UniProtKB/Swiss-Prot;Acc:Q6ZW35]
  ENSG00000214646
  ENSG00000099260	PALMD	palmdelphin_[Source:HGNC_Symbol;Acc:15846]
  ENSG00000115138	POMC	proopiomelanocortin_[Source:HGNC_Symbol;Acc:9201]
  ENSG00000136457	CHAD	chondroadherin_[Source:HGNC_Symbol;Acc:1909]
  ENSG00000140287	HDC	histidine_decarboxylase_[Source:HGNC_Symbol;Acc:4855]
  ENSG00000187323	DCC	deleted_in_colorectal_carcinoma_[Source:HGNC_Symbol;Acc:2701]
  ENSG00000238243	OR2W3	olfactory_receptor,family2,subfamilyW,member3_[Source:HGNC_Symbol;Acc:15021]
  ENSG00000001561	ENPP4	ectonucleotide_pyrophosphatase/phosphodiesterase_4_(putative)_[Source:HGNC_Symbol;Acc:3359]
  ENSG00000106852	LHX6	LIM_homeobox_6_[Source:HGNC_Symbol;Acc:21735]
  ENSG00000139537	CCDC65	coiled-coil_domain_containing_65_[Source:HGNC_Symbol;Acc:29937]
  ENSG00000183671	GPR1	G_protein-coupled_receptor_1_[Source:HGNC_Symbol;Acc:4463]
  ENSG00000197565	COL4A6	collagen,typeIV,alpha6_[Source:HGNC_Symbol;Acc:2208]
  ENSG00000179520	SLC17A8	solute_carrier_family_17_(sodium-dependent_inorganic_phosphate_cotransporter),member8_[Source:HGNC_Symbol;Acc:20151]
  ENSG00000148935	GAS2	growth_arrest-specific_2_[Source:HGNC_Symbol;Acc:4167]
  ENSG00000183111	ARHGEF37	Rho_guanine_nucleotide_exchange_factor_(GEF)37[Source:HGNC_Symbol;Acc:34430]
  ENSG00000007944	MYLIP	myosin_regulatory_light_chain_interacting_protein_[Source:HGNC_Symbol;Acc:21155]
  ENSG00000139278	GLIPR1	GLI_pathogenesis-related_1_[Source:HGNC_Symbol;Acc:17001]
  ENSG00000162722	TRIM58	tripartite_motif_containing_58_[Source:HGNC_Symbol;Acc:24150]
  ENSG00000157005	SST	somatostatin_[Source:HGNC_Symbol;Acc:11329]
  ENSG00000086300	SNX10	sorting_nexin_10_[Source:HGNC_Symbol;Acc:14974]
  ENSG00000100433	KCNK10	potassium_channel,subfamilyK,member10_[Source:HGNC_Symbol;Acc:6273]
  ENSG00000137877	SPTBN5	spectrin,beta,non-erythrocytic_5_[Source:HGNC_Symbol;Acc:15680]
  ENSG00000006283	CACNA1G	calcium_channel,voltage-dependent,T_type,alpha1G_subunit_[Source:HGNC_Symbol;Acc:1394]
  ENSG00000087303	NID2	nidogen_2_(osteonidogen)_[Source:HGNC_Symbol;Acc:13389]
  ENSG00000141449	GREB1L	growth_regulation_by_estrogen_in_breast_cancer-like_[Source:HGNC_Symbol;Acc:31042]
  ENSG00000198822	GRM3	glutamate_receptor,metabotropic3_[Source:HGNC_Symbol;Acc:4595]
  ENSG00000164418	GRIK2	glutamate_receptor,ionotropic,kainate_2_[Source:HGNC_Symbol;Acc:4580]
  ENSG00000181234	TMEM132C	transmembrane_protein_132C_[Source:HGNC_Symbol;Acc:25436]
  ENSG00000213088	DARC	Duffy_blood_group,chemokinereceptor_[Source:HGNC_Symbol;Acc:4035]
  ENSG00000183287	CCBE1	collagen_and_calcium_binding_EGF_domains_1_[Source:HGNC_Symbol;Acc:29426]
  ENSG00000170561	IRX2	iroquois_homeobox_2_[Source:HGNC_Symbol;Acc:14359]
  ENSG00000174599	TRAM1L1	translocation_associated_membrane_protein_1-like_1_[Source:HGNC_Symbol;Acc:28371]
  ENSG00000077942	FBLN1	fibulin_1_[Source:HGNC_Symbol;Acc:3600]
  ENSG00000170091	NA	Neuron-specific_protein_family_member_2_[Source:UniProtKB/Swiss-Prot;Acc:Q9Y328]
  ENSG00000229415	SFTA3	surfactant_associated_3_[Source:HGNC_Symbol;Acc:18387]
  ENSG00000204335	SP5	Sp5_transcription_factor_[Source:HGNC_Symbol;Acc:14529]
  ENSG00000163251	FZD5	frizzled_family_receptor_5_[Source:HGNC_Symbol;Acc:4043]
  ENSG00000196083	IL1RAP	interleukin_1_receptor_accessory_protein_[Source:HGNC_Symbol;Acc:5995]
  ENSG00000127528	KLF2	Kruppel-like_factor_2_(lung)_[Source:HGNC_Symbol;Acc:6347]
  ENSG00000173848	NET1	neuroepithelial_cell_transforming_1_[Source:HGNC_Symbol;Acc:14592]
  ENSG00000056291	NPFFR2	neuropeptide_FF_receptor_2_[Source:HGNC_Symbol;Acc:4525]
  ENSG00000084628	NKAIN1	Na+/K+transportingATPase_interacting_1_[Source:HGNC_Symbol;Acc:25743]
  ENSG00000169302	STK32A	serine/threonine_kinase_32A_[Source:HGNC_Symbol;Acc:28317]
  ENSG00000234409
  ENSG00000137968	SLC44A5	solute_carrier_family_44,member5_[Source:HGNC_Symbol;Acc:28524]
  ENSG00000104368	PLAT	plasminogen_activator,tissue[Source:HGNC_Symbol;Acc:9051]
  ENSG00000164574	GALNT10	UDP-N-acetyl-alpha-D-galactosamine:polypeptide_N-acetylgalactosaminyltransferase_10_(GalNAc-T10)_[Source:HGNC_Symbol;Acc:19873]
  ENSG00000101986	ABCD1	ATP-binding_cassette,sub-familyD_(ALD),member1_[Source:HGNC_Symbol;Acc:61]
  ENSG00000137166	FOXP4	forkhead_box_P4_[Source:HGNC_Symbol;Acc:20842]
  ENSG00000148798	INA	internexin_neuronal_intermediate_filament_protein,alpha[Source:HGNC_Symbol;Acc:6057]
  ENSG00000114923	SLC4A3	solute_carrier_family_4,anionexchanger,member3_[Source:HGNC_Symbol;Acc:11029]
  ENSG00000134508	CABLES1	Cdk5_and_Abl_enzyme_substrate_1_[Source:HGNC_Symbol;Acc:25097]
  ENSG00000138083	SIX3	SIX_homeobox_3_[Source:HGNC_Symbol;Acc:10889]
  ENSG00000170891	CYTL1	cytokine-like_1_[Source:HGNC_Symbol;Acc:24435]
  ENSG00000181744	C3orf58	chromosome_3_open_reading_frame_58_[Source:HGNC_Symbol;Acc:28490]
  ENSG00000198189	HSD17B11	hydroxysteroid_(17-beta)dehydrogenase11_[Source:HGNC_Symbol;Acc:22960]
  ENSG00000166426	CRABP1	cellular_retinoic_acid_binding_protein_1_[Source:HGNC_Symbol;Acc:2338]
  ENSG00000182771	GRID1	glutamate_receptor,ionotropic,delta_1_[Source:HGNC_Symbol;Acc:4575]
  ENSG00000076356	PLXNA2	plexin_A2_[Source:HGNC_Symbol;Acc:9100]
  ENSG00000170677	SOCS6	suppressor_of_cytokine_signaling_6_[Source:HGNC_Symbol;Acc:16833]
  ENSG00000159921	GNE	glucosamine_(UDP-N-acetyl)-2-epimerase/N-acetylmannosamine_kinase_[Source:HGNC_Symbol;Acc:23657]
  ENSG00000111145	ELK3	ELK3,ETS-domainprotein_(SRF_accessory_protein_2)_[Source:HGNC_Symbol;Acc:3325]
  ENSG00000119042	SATB2	SATB_homeobox_2_[Source:HGNC_Symbol;Acc:21637]
  ENSG00000254402	LRRC24	leucine_rich_repeat_containing_24_[Source:HGNC_Symbol;Acc:28947]
  ENSG00000106799	TGFBR1	transforming_growth_factor,betareceptor_1_[Source:HGNC_Symbol;Acc:11772]
  ENSG00000151692	RNF144A	ring_finger_protein_144A_[Source:HGNC_Symbol;Acc:20457]
  ENSG00000158106	RHPN1	rhophilin,RhoGTPase_binding_protein_1_[Source:HGNC_Symbol;Acc:19973]
  ENSG00000112414	GPR126	G_protein-coupled_receptor_126_[Source:HGNC_Symbol;Acc:13841]
  ENSG00000145147	SLIT2	slit_homolog_2_(Drosophila)_[Source:HGNC_Symbol;Acc:11086]
  ENSG00000136352	NKX2-1	NK2_homeobox_1_[Source:HGNC_Symbol;Acc:11825]
  ENSG00000126016	AMOT	angiomotin_[Source:HGNC_Symbol;Acc:17810]
  ENSG00000148824	NA	Mitochondrial_GTPase_1_[Source:UniProtKB/Swiss-Prot;Acc:Q9BT17]
  ENSG00000162627	SNX7	sorting_nexin_7_[Source:HGNC_Symbol;Acc:14971]
  ENSG00000146950	SHROOM2	shroom_family_member_2_[Source:HGNC_Symbol;Acc:630]
  ENSG00000162706	CADM3	cell_adhesion_molecule_3_[Source:HGNC_Symbol;Acc:17601]
  ENSG00000163110	PDLIM5	PDZ_and_LIM_domain_5_[Source:HGNC_Symbol;Acc:17468]
  ENSG00000110108	TMEM109	transmembrane_protein_109_[Source:HGNC_Symbol;Acc:28771]
  ENSG00000169116	PARM1	prostate_androgen-regulated_mucin-like_protein_1_[Source:HGNC_Symbol;Acc:24536]
  ENSG00000169184	MN1	meningioma_(disrupted_in_balanced_translocation)1[Source:HGNC_Symbol;Acc:7180]
  ENSG00000213390	ARHGAP19	Rho_GTPase_activating_protein_19_[Source:HGNC_Symbol;Acc:23724]
  ENSG00000104332	SFRP1	secreted_frizzled-related_protein_1_[Source:HGNC_Symbol;Acc:10776]
  ENSG00000132561	MATN2	matrilin_2_[Source:HGNC_Symbol;Acc:6908]
  ENSG00000144730	IL17RD	interleukin_17_receptor_D_[Source:HGNC_Symbol;Acc:17616]
  ENSG00000254706
  ENSG00000154146	NRGN	neurogranin_(protein_kinase_C_substrate,RC3)[Source:HGNC_Symbol;Acc:8000]
  ENSG00000101608	MYL12A	myosin,lightchain_12A,regulatory,non-sarcomeric_[Source:HGNC_Symbol;Acc:16701]
  ENSG00000188559	RALGAPA2	Ral_GTPase_activating_protein,alphasubunit_2_(catalytic)_[Source:HGNC_Symbol;Acc:16207]
  ENSG00000106484	MEST	mesoderm_specific_transcript_homolog_(mouse)_[Source:HGNC_Symbol;Acc:7028]
  ENSG00000065320	NTN1	netrin_1_[Source:HGNC_Symbol;Acc:8029]
  ENSG00000182580	EPHB3	EPH_receptor_B3_[Source:HGNC_Symbol;Acc:3394]

Stage-specific DE gene shared by Crotex and GE

1. GW13-15:UP, GW15-17:UP;
   No genes
   
2. GW13-15:UP, GW15-17:DN;
   

   id	name	description
   ENSG00000168542	COL3A1	collagen,typeIII,alpha1_[Source:HGNC_Symbol;Acc:2201]
   ENSG00000133636	NTS	neurotensin_[Source:HGNC_Symbol;Acc:8038]
   ENSG00000066032	CTNNA2	catenin_(cadherin-associated_protein),alpha2_[Source:HGNC_Symbol;Acc:2510]
   ENSG00000135063	FAM189A2	family_with_sequence_similarity_189,memberA2_[Source:HGNC_Symbol;Acc:24820]
   ENSG00000214401
   ENSG00000099984	GSTT2	glutathione_S-transferase_theta_2_[Source:HGNC_Symbol;Acc:4642]
   ENSG00000238083	LRRC37A2	leucine_rich_repeat_containing_37,memberA2_[Source:HGNC_Symbol;Acc:32404]
   ENSG00000101255	TRIB3	tribbles_homolog_3_(Drosophila)_[Source:HGNC_Symbol;Acc:16228]
   ENSG00000160284	C21orf56	chromosome_21_open_reading_frame_56_[Source:HGNC_Symbol;Acc:1298]

3. GW13-15:DN, GW15-17:UP;

   id	name	description
   ENSG00000022556	NLRP2	NLR_family,pyrindomain_containing_2_[Source:HGNC_Symbol;Acc:22948]
   ENSG00000225607	NA	Uncharacterized_proteincDNA_FLJ60024,highlysimilar_to_Cytochrome_P450_4F12__[Source:UniProtKB/TrEMBL;Acc:B4DNA9]
   ENSG00000147813	NAPRT1	nicotinate_phosphoribosyltransferase_domain_containing_1_[Source:HGNC_Symbol;Acc:30450]
   ENSG00000167654	ATCAY	ataxia,cerebellar,Cayman_type_[Source:HGNC_Symbol;Acc:779]

4. GW13-15:DN, GW15-17:DN;
   No genes
   
5. GW13-15:UP, GW15-17:not DE;

   id	name	description
   ENSG00000149054	ZNF215	zinc_finger_protein_215_[Source:HGNC_Symbol;Acc:13007]
   ENSG00000215845	TSTD1	thiosulfate_sulfurtransferase_(rhodanese)-like_domain_containing_1_[Source:HGNC_Symbol;Acc:35410]
   ENSG00000100336	APOL4	apolipoprotein_L,4[Source:HGNC_Symbol;Acc:14867]
   ENSG00000163823	CCR1	chemokine_(C-C_motif)receptor1_[Source:HGNC_Symbol;Acc:1602]
   ENSG00000169220	RGS14	regulator_of_G-protein_signaling_14_[Source:HGNC_Symbol;Acc:9996]
   ENSG00000203804	C1orf138	chromosome_1_open_reading_frame_138_[Source:HGNC_Symbol;Acc:32041]
   ENSG00000204520	MICA	MHC_class_I_polypeptide-related_sequence_A_[Source:HGNC_Symbol;Acc:7090]
   ENSG00000080573	COL5A3	collagen,typeV,alpha3_[Source:HGNC_Symbol;Acc:14864]
   ENSG00000165379	LRFN5	leucine_rich_repeat_and_fibronectin_type_III_domain_containing_5_[Source:HGNC_Symbol;Acc:20360]
   ENSG00000213402	PTPRCAP	protein_tyrosine_phosphatase,receptortype,C-associatedprotein_[Source:HGNC_Symbol;Acc:9667]
   ENSG00000139155	SLCO1C1	solute_carrier_organic_anion_transporter_family,member1C1_[Source:HGNC_Symbol;Acc:13819]
   ENSG00000187773	FAM69C	family_with_sequence_similarity_69,memberC_[Source:HGNC_Symbol;Acc:31729]
   ENSG00000133216	EPHB2	EPH_receptor_B2_[Source:HGNC_Symbol;Acc:3393]
   ENSG00000119737	GPR75	G_protein-coupled_receptor_75_[Source:HGNC_Symbol;Acc:4526]
   ENSG00000126790	C14orf149	chromosome_14_open_reading_frame_149_[Source:HGNC_Symbol;Acc:20488]
   ENSG00000162733	DDR2	discoidin_domain_receptor_tyrosine_kinase_2_[Source:HGNC_Symbol;Acc:2731]
   ENSG00000108231	LGI1	leucine-rich,gliomainactivated_1_[Source:HGNC_Symbol;Acc:6572]
   ENSG00000161921	CXCL16	chemokine_(C-X-C_motif)ligand16_[Source:HGNC_Symbol;Acc:16642]
   ENSG00000119673	ACOT2	acyl-CoA_thioesterase_2_[Source:HGNC_Symbol;Acc:18431]
   ENSG00000135046	ANXA1	annexin_A1_[Source:HGNC_Symbol;Acc:533]
   ENSG00000215790	SLC35E2	solute_carrier_family_35,memberE2_[Source:HGNC_Symbol;Acc:20863]
   ENSG00000157150	TIMP4	TIMP_metallopeptidase_inhibitor_4_[Source:HGNC_Symbol;Acc:11823]
   ENSG00000170579	DLGAP1	discs,large(Drosophila)homolog-associatedprotein_1_[Source:HGNC_Symbol;Acc:2905]
   ENSG00000143252	SDHC	succinate_dehydrogenase_complex,subunitC,integralmembrane_protein,15kDa[Source:HGNC_Symbol;Acc:10682]
   ENSG00000107796	ACTA2	actin,alpha2,smoothmuscle,aorta[Source:HGNC_Symbol;Acc:130]
   ENSG00000124193	SRSF6	serine/arginine-rich_splicing_factor_6_[Source:HGNC_Symbol;Acc:10788]
   ENSG00000152661	GJA1	gap_junction_protein,alpha1,43kDa[Source:HGNC_Symbol;Acc:4274]
   ENSG00000184110	EIF3C	eukaryotic_translation_initiation_factor_3,subunitC_[Source:HGNC_Symbol;Acc:3279]

6. GW13-15:DN, GW15-17:not DE;

   id	name	description
   ENSG00000166923	GREM1	gremlin_1_[Source:HGNC_Symbol;Acc:2001]
   ENSG00000164123	C4orf45	chromosome_4_open_reading_frame_45_[Source:HGNC_Symbol;Acc:26342]
   ENSG00000008196	TFAP2B	transcription_factor_AP-2_beta_(activating_enhancer_binding_protein_2_beta)_[Source:HGNC_Symbol;Acc:11743]
   ENSG00000186897	C1QL4	complement_component_1,qsubcomponent-like_4_[Source:HGNC_Symbol;Acc:31416]
   ENSG00000054598	FOXC1	forkhead_box_C1_[Source:HGNC_Symbol;Acc:3800]
   ENSG00000104808	DHDH	dihydrodiol_dehydrogenase_(dimeric)_[Source:HGNC_Symbol;Acc:17887]
   ENSG00000124813	RUNX2	runt-related_transcription_factor_2_[Source:HGNC_Symbol;Acc:10472]
   ENSG00000173068	BNC2	basonuclin_2_[Source:HGNC_Symbol;Acc:30988]
   ENSG00000165929	TC2N	tandem_C2_domains,nuclear[Source:HGNC_Symbol;Acc:19859]
   ENSG00000157064	NMNAT2	nicotinamide_nucleotide_adenylyltransferase_2_[Source:HGNC_Symbol;Acc:16789]
   ENSG00000243244	STON1	stonin_1_[Source:HGNC_Symbol;Acc:17003]
   ENSG00000173809	TDRD12	tudor_domain_containing_12_[Source:HGNC_Symbol;Acc:25044]
   ENSG00000135333	EPHA7	EPH_receptor_A7_[Source:HGNC_Symbol;Acc:3390]
   ENSG00000231421
   ENSG00000168675	C18orf1	chromosome_18_open_reading_frame_1_[Source:HGNC_Symbol;Acc:1224]
   ENSG00000156395	SORCS3	sortilin-related_VPS10_domain_containing_receptor_3_[Source:HGNC_Symbol;Acc:16699]
   ENSG00000204103	MAFB	v-maf_musculoaponeurotic_fibrosarcoma_oncogene_homolog_B_(avian)_[Source:HGNC_Symbol;Acc:6408]
   ENSG00000168447	SCNN1B	sodium_channel,nonvoltage-gated1,beta[Source:HGNC_Symbol;Acc:10600]
   ENSG00000106546	AHR	aryl_hydrocarbon_receptor_[Source:HGNC_Symbol;Acc:348]
   ENSG00000117598	NA	Lipid_phosphate_phosphatase-related_protein_type_5_[Source:UniProtKB/Swiss-Prot;Acc:Q32ZL2]
   ENSG00000120322	PCDHB8	protocadherin_beta_8_[Source:HGNC_Symbol;Acc:8693]
   ENSG00000250305	NA	Putative_methyltransferase_KIAA1456_[Source:UniProtKB/Swiss-Prot;Acc:Q9P272]
   ENSG00000106868	SUSD1	sushi_domain_containing_1_[Source:HGNC_Symbol;Acc:25413]
   ENSG00000183943	PRKX	protein_kinase,X-linked[Source:HGNC_Symbol;Acc:9441]
   ENSG00000204060	FOXO6	forkhead_box_O6_[Source:HGNC_Symbol;Acc:24814]
   ENSG00000170941	NA	Uncharacterized_protein_KIAA1456_[Source:UniProtKB/Swiss-Prot;Acc:Q8N9K7]
   ENSG00000063438	AHRR	aryl-hydrocarbon_receptor_repressor_[Source:HGNC_Symbol;Acc:346]
   ENSG00000107902	LHPP	phospholysine_phosphohistidine_inorganic_pyrophosphate_phosphatase_[Source:HGNC_Symbol;Acc:30042]
   ENSG00000169436	COL22A1	collagen,typeXXII,alpha1_[Source:HGNC_Symbol;Acc:22989]
   ENSG00000184985	SORCS2	sortilin-related_VPS10_domain_containing_receptor_2_[Source:HGNC_Symbol;Acc:16698]
   ENSG00000163328	GPR155	G_protein-coupled_receptor_155_[Source:HGNC_Symbol;Acc:22951]
   ENSG00000173598	NUDT4	nudix_(nucleoside_diphosphate_linked_moiety_X)-type_motif_4_[Source:HGNC_Symbol;Acc:8051]
   ENSG00000114200	BCHE	butyrylcholinesterase_[Source:HGNC_Symbol;Acc:983]
   ENSG00000183722	LHFP	lipoma_HMGIC_fusion_partner_[Source:HGNC_Symbol;Acc:6586]
   ENSG00000139722	VPS37B	vacuolar_protein_sorting_37_homolog_B_(S.cerevisiae)[Source:HGNC_Symbol;Acc:25754]

7. GW13-15:not DE, GW15-17:UP;

   id	name	description
   ENSG00000145247	OCIAD2	OCIA_domain_containing_2_[Source:HGNC_Symbol;Acc:28685]
   ENSG00000070748	CHAT	choline_O-acetyltransferase_[Source:HGNC_Symbol;Acc:1912]
   ENSG00000165659	DACH1	dachshund_homolog_1_(Drosophila)_[Source:HGNC_Symbol;Acc:2663]
   ENSG00000165983	PTER	phosphotriesterase_related_[Source:HGNC_Symbol;Acc:9590]
   ENSG00000139220	PPFIA2	protein_tyrosine_phosphatase,receptortype,fpolypeptide_(PTPRF),interactingprotein_(liprin),alpha2_[Source:HGNC_Symbol;Acc:9246]
   ENSG00000147255	IGSF1	immunoglobulin_superfamily,member1_[Source:HGNC_Symbol;Acc:5948]
   ENSG00000146233	CYP39A1	cytochrome_P450,family39,subfamilyA,polypeptide1_[Source:HGNC_Symbol;Acc:17449]
   ENSG00000181649	PHLDA2	pleckstrin_homology-like_domain,familyA,member2_[Source:HGNC_Symbol;Acc:12385]
   ENSG00000204516	MICB	MHC_class_I_polypeptide-related_sequence_B_[Source:HGNC_Symbol;Acc:7091]
   ENSG00000164692	COL1A2	collagen,typeI,alpha2_[Source:HGNC_Symbol;Acc:2198]
   ENSG00000114805	PLCH1	phospholipase_C,eta1_[Source:HGNC_Symbol;Acc:29185]
   ENSG00000051523	CYBA	cytochrome_b-245,alphapolypeptide_[Source:HGNC_Symbol;Acc:2577]
   ENSG00000145703	IQGAP2	IQ_motif_containing_GTPase_activating_protein_2_[Source:HGNC_Symbol;Acc:6111]
   ENSG00000165072	MAMDC2	MAM_domain_containing_2_[Source:HGNC_Symbol;Acc:23673]
   ENSG00000130558	OLFM1	olfactomedin_1_[Source:HGNC_Symbol;Acc:17187]
   ENSG00000120318	ARAP3	ArfGAP_with_RhoGAP_domain,ankyrinrepeat_and_PH_domain_3_[Source:HGNC_Symbol;Acc:24097]
   ENSG00000198750	GATSL2	GATS_protein-like_2_[Source:HGNC_Symbol;Acc:37073]
   ENSG00000162849	KIF26B	kinesin_family_member_26B_[Source:HGNC_Symbol;Acc:25484]
   ENSG00000134333	LDHA	lactate_dehydrogenase_A_[Source:HGNC_Symbol;Acc:6535]
   ENSG00000064666	CNN2	calponin_2_[Source:HGNC_Symbol;Acc:2156]

8. GW13-15:not DE, GW15-17:DN;

   id	name	description
   ENSG00000259210
   ENSG00000198650	TAT	tyrosine_aminotransferase_[Source:HGNC_Symbol;Acc:11573]
   ENSG00000163053	SLC16A14	solute_carrier_family_16,member14_(monocarboxylic_acid_transporter_14)_[Source:HGNC_Symbol;Acc:26417]
   ENSG00000125637	PSD4	pleckstrin_and_Sec7_domain_containing_4_[Source:HGNC_Symbol;Acc:19096]
   ENSG00000153822	KCNJ16	potassium_inwardly-rectifying_channel,subfamilyJ,member16_[Source:HGNC_Symbol;Acc:6262]
   ENSG00000188803	SHISA6	shisa_homolog_6_(Xenopus_laevis)_[Source:HGNC_Symbol;Acc:34491]
   ENSG00000127952	STYXL1	serine/threonine/tyrosine_interacting-like_1_[Source:HGNC_Symbol;Acc:18165]
   ENSG00000150907	FOXO1	forkhead_box_O1_[Source:HGNC_Symbol;Acc:3819]
   ENSG00000076344	RGS11	regulator_of_G-protein_signaling_11_[Source:HGNC_Symbol;Acc:9993]
   ENSG00000174938	SEZ6L2	seizure_related_6_homolog_(mouse)-like_2_[Source:HGNC_Symbol;Acc:30844]
   ENSG00000122694	GLIPR2	GLI_pathogenesis-related_2_[Source:HGNC_Symbol;Acc:18007]
   ENSG00000167774	NDUFA7	NADH_dehydrogenase_(ubiquinone)1alpha_subcomplex,7,14.5kDa_[Source:HGNC_Symbol;Acc:7691]
   ENSG00000132164	SLC6A11	solute_carrier_family_6_(neurotransmitter_transporter,GABA),member_11_[Source:HGNC_Symbol;Acc:11044]

DAVID enrichment for DE genes

• GW associated DE genes shared by cell types show no enrichment due to small gene lists.
  
• GW15 vs GW 13: calcium ion binding in cortex UP and GE DN, neurogenesis in cortex DN.
  
• GW17 vs GW 15: neurogenesis in GE, no enrichment in cortex.
  
• GW17 vs GW 13: calcium ion binding in cortex UP and GE UP, neurogenesis in GE DN.
  

Isoform analysis

• On average, there are NA isoform genes between 13- and 17-week individuals, majority of them are shared among different comparisons and between the two cell types (hypergeometric p-value = 0).
  
• There are 2878 isoform genes in cortex supported by at least two comparisons, and 2505 in GE, among them, 1800 isoform genes are shared between the two cell types.
  
• Isoform genes are enriched in cell signaling related terms.

Sample	DE_genes	DE_exons	with_expressed_genes	isoform_exons	exclude_DE_genes	isoform_genes	GW
Cortex-HuFNSC01_Cortex-HuFNSC03	565	28637	16045	8044	7772	2490	17 vs 15
Cortex-HuFNSC01_Cortex-HuFNSC04	530	27428	13200	6365	6134	2167	17 vs 13
Cortex-HuFNSC02_Cortex-HuFNSC03	681	28963	16765	7961	7630	2425	17 vs 15
Cortex-HuFNSC02_Cortex-HuFNSC04	722	29416	13894	6351	6011	2105	17 vs 13
Cortex-HuFNSC03_Cortex-HuFNSC04	642	26826	12185	5818	5479	1994	15 vs 13
GE-HuFNSC01_GE-HuFNSC03	861	31361	14725	5880	5458	2041	17 vs 15
GE-HuFNSC01_GE-HuFNSC04	883	34359	15889	6401	5996	2049	17 vs 13
GE-HuFNSC02_GE-HuFNSC03	921	32827	15557	5773	5306	1965	17 vs 15
GE-HuFNSC02_GE-HuFNSC04	869	34699	16012	6113	5711	1986	17 vs 13
GE-HuFNSC03_GE-HuFNSC04	545	24752	12223	4582	4422	1454	15 vs 13